Circadian disruption caused by lifestyle factors such as mistimed eating and shift work is increasingly recognized as a contributor to metabolic disorders, including type 2 diabetes (1, 2). Dietary polyphenols, plant-derived bioactive compounds abundant in fruits and vegetables, have emerged as potential nutritional modulators of circadian and metabolic health. Evidence from our recent human intervention suggests that the metabolic responses to polyphenol-rich dietary interventions may depend on timing of intake (3); however, the molecular mechanisms underlying these time-dependent responses remain unclear (4). This study investigated the effects of quercetin and its methylated metabolite isorhamnetin on disrupted clock gene expression and related phosphorylation events in a human hepatocyte model following best practice recommendations for polyphenol and circadian studies (4). HepG2 cells were synchronized with a 2-hour serum shock to align their circadian oscillations and exposed to metabolic stress (0.2 mM hydrogen peroxide and 25 mM glucose), with or without a single or repeated dose of quercetin or isorhamnetin (10 μM). Clock gene expression was measured every four hours during the second 24-h cycle, with additional analysis at 34 h and 46 h, with phosphoproteomic profiling at 15 min and 34 h. Gene expression was analyzed by one-way ANOVA with Dunnett's multiple comparisons test (p < 0.05). Phosphoproteomic data were analyzed using variance-stabilizing normalization and Benjamini–Hochberg false discovery rate correction, with significance defined as adjusted p < 0.05 and log₂ fold change ≥ 1. Repeated, but not single, exposure to quercetin or isorhamnetin at 34 and 46 h significantly modulated RORα expression, a key transcriptional regulator of some circadian genes. Phosphoproteomic analysis at 34 h, using quercetin, identified 325 differentially regulated phosphosites among 23,665 quantified sites (1.37%), with significant changes observed only after repeated exposure. Notably, repeated quercetin treatment did not affect phosphorylation of core clock-encoded proteins but significantly remodeled the phosphorylation of non-clock and circadian proteins involved in metabolic signaling and cellular regulatory pathways. These findings demonstrate that cellular response to quercetin and isorhamnetin depends on the number of doses, with repeated exposure selectively regulating circadian gene expression and kinase-based signaling networks. This study provides mechanistic insight into how habitual dietary polyphenol consumption may interact with circadian-metabolic pathways and supports further investigation of nutritional strategies to improve circadian and metabolic health through meal timing and bioactive food components.